FIRMA: a method for detection of alternative splicing from exon array data

摘要: Motivation: Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent exon and tiling microarrays means researchers now have the capacity to experimentally measure on a genome wide level. New methods are needed analyze from these arrays. Results: We present method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential in array data. FIRMA has been developed Affymetrix arrays, but could principle be extended other arrays or splice junction arrays. evaluated method simulated data, also applied it two datasets: panel 11 human tissues set 10 pairs matched normal tumor colon tissue. able detect exons several genes confirmed by reverse transcriptase PCR. Availability: R code implementing our contributed package aroma.affymetrix. Contact: epurdom/at/stat.berkeley.edu Supplementary information: Supplementary available at Bioinformatics online.